NOL11

nucleolar protein 11, the group of UTPa subcomplex|Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): 17:67717931-67744531

Links

ENSG00000130935 ∙ NCBI:25926 ∙ OMIM:615366 ∙ HGNC:24557 ∙ Uniprot:Q9H8H0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NOL11 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NOL11 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			58	3	1	62
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	58	3	2

Variants in NOL11

This is a list of pathogenic ClinVar variants found in the NOL11 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
17-67717958-T-C		not specified	Uncertain significance (Nov 30, 2021)
17-67717965-A-T		not specified	Uncertain significance (Mar 02, 2023)
17-67717966-G-A		not specified	Uncertain significance (Feb 27, 2025)
17-67717993-A-G		not specified	Likely benign (Aug 15, 2023)
17-67718002-C-T		not specified	Uncertain significance (Mar 26, 2024)
17-67718012-T-C		not specified	Uncertain significance (Aug 20, 2024)
17-67718023-G-A		not specified	Uncertain significance (May 04, 2023)
17-67718024-A-C		not specified	Uncertain significance (Sep 27, 2024)
17-67718045-A-C		not specified	Uncertain significance (Jan 06, 2023)
17-67718059-G-T		not specified	Uncertain significance (Nov 25, 2024)
17-67719690-C-G		not specified	Uncertain significance (Dec 19, 2023)
17-67719717-G-A		not specified	Uncertain significance (Jun 11, 2021)
17-67719721-A-T		not specified	Uncertain significance (Aug 12, 2021)
17-67719737-G-A		not specified	Uncertain significance (Apr 18, 2023)
17-67719759-G-A		not specified	Uncertain significance (Aug 21, 2023)
17-67719765-A-C		not specified	Uncertain significance (Jan 03, 2022)
17-67719906-G-A		not specified	Uncertain significance (Jul 17, 2024)
17-67719936-A-T		not specified	Uncertain significance (Feb 12, 2024)
17-67721405-T-C		not specified	Uncertain significance (May 07, 2024)
17-67721408-G-T		not specified	Uncertain significance (May 16, 2023)
17-67721440-G-T		not specified	Uncertain significance (Jun 29, 2023)
17-67721448-C-T		not specified	Uncertain significance (Dec 24, 2024)
17-67721454-G-A		not specified	Uncertain significance (May 03, 2023)
17-67721487-A-G		not specified	Uncertain significance (May 23, 2024)
17-67721494-T-G		not specified	Uncertain significance (Aug 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NOL11	protein_coding	protein_coding	ENST00000253247	18	26699

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.92e-7	1.00	125704	0	44	125748	0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.416	340	362	0.938	0.0000179	4683
Missense in Polyphen		68	86.682	0.78448		1252
Synonymous	-0.482	138	131	1.05	0.00000671	1347
Loss of Function	3.26	17	38.9	0.437	0.00000181	520

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000298	0.000217
Ashkenazi Jewish	0.000412	0.000397
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000244	0.000237
Middle Eastern	0.000163	0.000163
South Asian	0.000137	0.000131
Other	0.000329	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Ribosome biogenesis factor. May be required for both optimal rDNA transcription and small subunit (SSU) pre-rRNA processing at sites A', A0, 1 and 2b. {ECO:0000269|PubMed:22916032}.
• Pathway: rRNA processing;Metabolism of RNA;rRNA modification in the nucleus and cytosol;rRNA processing in the nucleus and cytosol (Consensus)

Recessive Scores

• pRec: 0.0798

Intolerance Scores

• loftool: 0.792
• rvis_EVS: 0.29
• rvis_percentile_EVS: 71.57

Haploinsufficiency Scores

• pHI: 0.498
• hipred: N
• hipred_score: 0.368
• ghis: 0.608

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.737

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Nol11

Gene ontology

• Biological process: rRNA processing;maturation of SSU-rRNA;positive regulation of transcription of nucleolar large rRNA by RNA polymerase I
• Cellular component: nucleoplasm;nucleolus;t-UTP complex
• Molecular function: RNA binding;protein binding